US20060127935A1 - Identification and use of prognostic and predictive markers in cancer treatment - Google Patents

Identification and use of prognostic and predictive markers in cancer treatment Download PDF

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US20060127935A1
US20060127935A1 US11/300,869 US30086905A US2006127935A1 US 20060127935 A1 US20060127935 A1 US 20060127935A1 US 30086905 A US30086905 A US 30086905A US 2006127935 A1 US2006127935 A1 US 2006127935A1
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htpap
amplification
patient
breast cancer
her2
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Soonmyung Paik
Chungyeul Kim
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NSABP Foundation Inc
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Definitions

  • Breast cancer is a heterogeneous disease with respect to clinical behavior and response to therapy. This variability is a result of the differing molecular make up of cancer cells within each subtype of breast cancer.
  • estrogen receptor and HER2 which are targets of antiestrogens and Herceptin respectively. Efforts to target these two molecules have been proven to be extremely productive. Nevertheless, those tumors that do not have these two targets are often treated with chemotherapy which generally targets proliferating cells. Since some important normal cells are also proliferating, they are damaged by chemotherapy at the same time. Therefore, chemotherapy is associated with severe toxicity. Identification of molecular targets in tumors in addition to ER or HER2 is critical in the development of new anticancer therapy.
  • CGH comparative genomic hybridization
  • Hyman et al have examined correlation between copy number changes and expression levels in 14 breast cancer cell lines using cDNA microarray of 13,824 genes.
  • Hyman E Kauraniemi P, Hautaniemi S et al., Cancer Res 2002; 62(21):6240-6245. They found 44% of highly amplified genes resulted in overexpression with 10.5% of overexpressed genes being amplified.
  • FISH is a stable method that works with formalin fixed paraffin embedded sections in a routing clinical setting.
  • FISH probes for HER2 have been FDA approved as a predictive test for Herceptin response. Due to the stability of DNA in the paraffin embedded sections, it is more reliable than RNA based or immunohistochemistry based clinical assays.
  • FISH probes for potentially important amplified genes have not been comprehensively developed. In fact, there is only one vendor (Vysis, Downers Grove, Ill.) that supplies an array of probes but most of these probes have not been clinically validated at this point as prognostic factors. These probes are also very expensive (cost about $300 per case) and of limited variety, barely scratching the repertoire of potentially important amplicons in solid tumors such as breast and colon cancer.
  • HER2 protein Approximately 15 to 20% of all breast cancer has overexpression of HER2 protein on its cell surface. Paik S, Hazan R, Fisher E R et al., J Clin Oncol 1990; 8(1):103-112. Such tumors are known to have a worse prognosis than those without HER2 protein overexpression Paik S, Hazan R, Fisher E R et al., J Clin Oncol 1990; 8(1):103-112. Overexpression of HER2 protein is almost invariably due to amplification or increased copy number of gene encoding HER2.
  • trastuzumab Herceptin
  • Herceptin has recently been shown to be effective in prolonging survival in patients diagnosed with advanced breast cancer with HER2 overexpression. Slamon D J, Leyland-Jones B, Shak S et al., N Engl J Med 2001; 344(11):783-792. Recently it has also been shown to reduce recurrences and death in patients with early stage breast cancer which have HER2 protein overexpression or HER2 gene amplification Romond E H, Pesez E A, Bryant J et.
  • cMYC has an important role as a molecular switch that determines the cell's fate to go through programmed cell death or cell proliferation
  • Pelengaris S Khan M, Evan G., Nat Rev Cancer 2002; 2(10):764-776
  • Pelengaris S Khan M, Evan G I., Cell 2002; 109(3):321-334.
  • cMYC When cMYC is overexpressed, cells go into uncontrolled cell proliferation and become susceptible to programmed cell death in the absence of a survival signal (see FIG. 1 a ).
  • cMYC induces apoptosis by regulating many components of the programmed cell death pathway, but the main effector seems to be Bax.
  • Pelengaris S Khan M, Evan G., Nat Rev Cancer 2002; 2(10):764-776.
  • HTPAP gene which when amplified confers poor prognosis in breast cancer patients even after treatment with standard chemotherapy containing doxorubicin, cyclophosphamide, and paclitaxel.
  • HTPAP amplification is an independent prognosticator of tumor size, treatment, number of positive axillary lymph node, age and hormone receptor status, HER2 amplification, and cMYC amplification.
  • cMYC is a predictor of response to Herceptin, in such a way that for patients with cMYC amplification together with HER2 amplification/overexpression, there is a 75% reduction in cancer recurrence rate when Herceptin is added to chemotherapy, compared to only 45% reduction in recurrence rate for those patients without cMYC amplification.
  • cMYC is amplified in approximately 30% of the breast cancer patients with HER2 amplification or overexpression. Inhibition of HER2 signaling by Trastuzumab apparently changes the cMYC role from proliferation switch to pro-apoptotic switch.
  • the invention has the following clinical applications: optimization of methods for patient selection and determining treatments using Trastuzumab and other drugs that target a HER2 signaling pathway: optimization of methods for patient selection for future clinical studies that test the addition of other drugs or targeted therapies, such as Bevacizumab (Avastin) that targets angiogenesis, by allowing identification of patients who are at high risk of relapse even after Trastuzumab or HER2 targeted therapy: PCR-based assay that will detect the gene amplification status of both HER2 and cMYC in a single tube assay for prognostication and prediction of response in breast cancer patients: and rational development of cMYC targeted therapy through indirect modulation of its pro-apoptotic activity by inhibiting anti-apoptotic signal from other activated oncogenes.
  • targeted therapies such as Bevacizumab (Avastin) that targets angiogenesis
  • FIG. 1 a shows a schematic of cMYC as a pro-apoptotic switch.
  • FIG. 1 b shows a schematic of cMYC as a proliferation switch.
  • FIG. 1 c shows a schematic of an anti-apoptotic signal from HER2.
  • FIG. 2 shows a flow chart describing a method of identifying therapeutic targets
  • FIG. 3 shows the results of a clustering study.
  • FIG. 4 shows a chart of recurrence by amplification.
  • FIG. 5 shows a Kaplan Meier plot for APPBP2.
  • FIG. 6 shows a Kaplan Meier plot for BMP7.
  • FIG. 7 shows a Kaplan Meier plot for bm — 009.
  • FIG. 8 shows a Kaplan Meier plot for CACNB1.
  • FIG. 9 shows a Kaplan Meier plot for chk.
  • FIG. 10 shows a Kaplan Meier plot for c_myc.
  • FIG. 11 shows a Kaplan Meier plot for cyclind1.
  • FIG. 12 shows a Kaplan Meier plot for decr1.
  • FIG. 13 shows a Kaplan Meier plot for FLJ 10783.
  • FIG. 14 shows a Kaplan Meier plot for GRO1.
  • FIG. 15 shows a Kaplan Meier plot for GRB2.
  • FIG. 16 shows a Kaplan Meier plot for HBS1L.
  • FIG. 17 shows a Kaplan Meier plot for HER2.
  • FIG. 18 shows a Kaplan Meier plot for MAL2.
  • FIG. 19 shows a Kaplan Meier plot for HTPAP.
  • FIG. 20 shows a Kaplan Meier plot for MLN64.
  • FIG. 21 shows a Kaplan Meier plot for MRPS7.
  • FIG. 22 shows a Kaplan Meier plot for PPM1D.
  • FIG. 23 shows a Kaplan Meier plot for NCO43.
  • FIG. 24 shows a Kaplan Meier plot for RPS6KB1.
  • FIG. 25 shows a Kaplan Meier plot for SEB4D.
  • FIG. 26 shows a Kaplan Meier plot for stk6.
  • FIG. 27 shows a Kaplan Meier plot for SIP2 — 28.
  • FIG. 28 shows a Kaplan Meier plot for TPD52
  • FIG. 29 shows a Kaplan Meier plot for TRAF4.
  • FIG. 30 shows a Kaplan Meier plot for ZNF217.
  • FIG. 31 shows a Kaplan Meier plot for ZHX1.
  • FIG. 32 shows a Kaplan Meier plot for any amplicon.
  • FIG. 33 shows a diagram of the HTPAP gene.
  • FIG. 34 shows a recurrence free survival.
  • BAC directly fluorescence labeling bacterial artificial clones
  • This disclosure provides a method for fluorescently labeling BAC clones representing known amplicons efficiently by combining a series of whole genome amplification methods and an efficient FISH method for paraffin embedded tissue which has been archived more than 10 years (see overview in FIG. 2 ).
  • This labeling and FISH method is a log order less expensive as compared to commercially available probes. Using paraffin block tissue samples for over 30,000 breast and colon cancer cases that are all annotated with clinical follow up information and treatment received provided a unique source for clinical correlative science studies.
  • TMA tissue micro array
  • tissue microarrays were constructed and FISH assays performed for 10 different in-housed developed probes based on array CGH data (two sets are very close to each other, i.e. HER2 and MLN64, APPBP2 and PPM1D).
  • Amplification status was categorized as either amplified or non-amplified, with gene amplification defined as having more than 4 signals (4 dots per single tumor cell nucleus) from in situ hybridization.
  • Correlation with clinical outcome using univariate Cox proportional hazard model showed that HER2, MLN64 (which is very close to HER2 and highly correlated), cMYC, HTPAP, TPD52, MAL2, and ZNF217 are significantly correlated with clinical outcome of patients entered into the B-28 trial (Table 1).
  • the presence of any amplification and number of amplifications also showed significant correlation with outcome.
  • Kaplan Meier plots for each of the 27 amplicons screened are shown in the FIGS. 5 to 31 .
  • a Kaplan Meier plot comparing cases with no amplification versus any amplification is shown in FIG. 32 .
  • Multivariate analysis including conventional prognostic markers (tumor size, number of positive nodes, hormone receptor status, and age) was performed. Three amplicons remained significant: HER2; cMYC; and HTPAP (as shown in Table 2).
  • HTPAP is a novel gene which translates into a protein with a phosphatidic acid phosphatase homology domain and a 5′ transmembrane domains as well as signal peptide that indicates that the protein product is secreted ( FIG. 33 ).
  • the Bacterial Artificial Chromosome clone used for generation of FISH probe for HTPAP (clone RP11-513D5) has only three genes in it: HTPAP; WHSC1L1; and DDHD2.
  • HTPAP is the one that is overexpressed when this region is amplified.
  • HTPAP is a novel gene which translates into a protein with a phosphatidic acid phosphatase homology domain and a 5′ transmembrane domains as well as signal peptide that indicates that the protein product is secreted ( FIG. 33 ).
  • HTPAP is amplified and stable clinical diagnostic assay using FISH or PCR can be used to detect the amplification status; 2) it is an independent prognostic factor in heavily treated patients; 3) it is transmembrane protein with enzyme activity; and 4) it is also secreted.
  • Certain embodiments of the present invention include monoclonal antibodies or series of monoclonal antibodies with specificity for the extracellular domain of the HTPAP protein. These antibodies can be used either alone or in combination with chemotherapeutic drugs or antibodies to other targets. The generation of such antibodies can be performed via any number of methods for monoclonal production which are well known in the art.
  • these anti-HTPAP antibodies used to detect HTPAP protein secreted in the serum or plasma or body fluid (such as nipple aspirate from the patients) and compared to normal levels in the diagnosis or monitoring of disease during therapy. Detection may be accomplished by any number of methods well known in the art, including but not limited to radioimmunoassay, flow cytometery, ELISA, or other colormetric assays.
  • Phosphatidic acid phosphatase domain typically acts as an important signaling molecule in the cancer cells. Certain embodiments of the present invention include the use of these domains of the HTPAP gene in targeting the development of small molecules that interfere or modulate such activity. Furthermore, the use of anti-bodies to HTPAP can be used to identify down stream signaling molecules to HTPAP and subsequently targeted by small molecule therapeutics.
  • Certain other embodiments include the blocking of HTPAP gene activity using siRNA, antisense oligonucleotide, or Ribozyme approaches that are well known in the art.
  • genes found to be of marginal prognostic power in this study cohort of AC or ACT Treated node positive breast cancer may have significant prognostic power in untreated or node negative patients—these include TPD52, MAL2, ZNF217, NCOA3, ZHX1, BM — 009, BMP7, and STK6 and they also may provide attractive target for therapeutic development.
  • three prognostic amplified genes HER2, cMYC, and HTPAP can be utilized to create a prognostic index to guide treatment decision making for breast cancer patients.
  • Certain other embodiments include same three genes together with clinical variables to generate a prognostic index to guide treatment decision making.
  • cMYC The status of cMYC in 1344 patients enrolled in the NSABP B-31 trial were examined to test the potential benefits of addition of Trastuzumab to chemotherapy in the treatment of patients diagnosed with early stage breast cancer with HER2 gene amplification/overexpression.
  • FISH was used to enumerate the cMYC gene copy number using a commercially available DNA probe (Vysis). Any tumor with more than 10% of cells showing more than 4 copies of cMYC gene was classified as cMYC gene amplified in this analysis. 399 cases out of 1344 total cases studied were classified as cMYC amplified.
  • Tumors with cMYC amplification were believed to be sensitive to inhibition of HER2 signaling due to its activation of a pro-apoptotic signal when the HER2 signal is inhibited by Trastuzumab and that this would translate into much more significant reduction in recurrence rate in cMYC amplified cohort in comparison to patients with no amplification of cMYC.
  • the present disclosure includes a method of determining a cancer patient's amplification of cMYC and HER2 status.
  • the present disclosure is also applicable to other HER2-targeted therapies since the effect is an indirect one through activation of pro-apoptotic role of cMYC.
  • the invention disclosed herein includes methods of determining treatments and treating patients with Trastuzumab and other materials based on a patient's cMYC and HER2 status.
  • the present invention can be applied in exploiting pro-apoptotic function of cMYC in cMYC amplified tumors without HER2 amplification.
  • cMYC pro-apoptotic function of cMYC in cMYC amplified tumors without HER2 amplification.
  • indirect approaches inhibiting survival signals will likely make such tumors go through programmed cell death by activation of cMYC's pro-apoptotic function.
  • the test for cMYC in the present disclosure can be either in the format of FISH, quantitative polymerase chain reaction, immunohistochemistry or other immunological detection method in homogenized tumor tissue, including a single tube, “real-time” quantitative polymerase chain reaction (at PCR) assay that includes HER2, cMYC, HTPAP, and a reference gene to simultaneously detect the presence of amplification of these three genes and provide both prognostic information as well as prediction of response to Trastuzumab or other HER2 targeted therapies, as well as the assay and methods of treating a patient based on the results of such an assay.
  • FISH quantitative polymerase chain reaction
  • immunohistochemistry immunological detection method in homogenized tumor tissue
  • a single tube “real-time” quantitative polymerase chain reaction (at PCR) assay that includes HER2, cMYC, HTPAP, and a reference gene to simultaneously detect the presence of amplification of these three genes and provide both prognostic information as well as prediction of response
  • the present invention can be applied in exploiting pro-apoptotic function of cMYC in cMYC amplified tumors without HER2 amplification.
  • cMYC pro-apoptotic function of cMYC in cMYC amplified tumors without HER2 amplification.
  • indirect approaches inhibiting survival signals will likely make such tumors go through programmed cell death by activation of cMYC's pro-apoptotic function.

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WO2009148593A1 (en) * 2008-06-02 2009-12-10 Nsabp Foundation, Inc. Identification and use of prognostic and predictive markers in cancer treatment
US9873742B2 (en) 2012-10-05 2018-01-23 Genentech, Inc. Methods for diagnosing and treating inflammatory bowel disease

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JP5433189B2 (ja) * 2007-09-28 2014-03-05 承一 尾崎 Ｍｐｏ−ａｎｃａ関連血管炎の被験者に対する治療の効果を予測する材料を提供する方法
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